read.experiment: Read ORFik 'experiment'

In JokingHero/ORFik: Open Reading Frames in Genomics

Read ORFik experiment

Description

Read in runs / samples from an experiment as a single R object. To read an ORFik experiment, you must of course make one first. See create.experiment The file must be csv and be a valid ORFik experiment

Usage

read.experiment(
  file,
  in.dir = ORFik::config()["exp"],
  validate = TRUE,
  output.env = .GlobalEnv
)

Arguments

file	relative path to a ORFik experiment. That is a .csv file following ORFik experiment style ("," as seperator). , or a template data.frame from create.experiment. Can also be full path to file, then in.dir argument is ignored.
in.dir	Directory to load experiment csv file from, default: ORFik::config()["exp"], which has default "~/Bio_data/ORFik_experiments/" Set to NULL if you don't want to save it to disc. Does not apply if file argument is not a path (can also be a data.frame). Also does not apply if file argument was given as full path.
validate	logical, default TRUE. Abort if any library files does not exist. Do not set this to FALSE, unless you know what you are doing!
output.env	an environment, default .GlobalEnv. Which environment should ORFik output libraries to (if this is done), can be updated later with envExp(df) <- new.env().

Value

an ORFik experiment

See Also

Other ORFik_experiment: ORFik.template.experiment(), ORFik.template.experiment.zf(), bamVarName(), create.experiment(), experiment-class, filepath(), libraryTypes(), organism,experiment-method, outputLibs(), save.experiment(), validateExperiments()

Examples

# From file
## Not run: 
# Read from file
df <- read.experiment(filepath) # <- valid ORFik .csv file

## End(Not run)
## Read from (create.experiment() template)
df <- ORFik.template.experiment()

## To save it, do:
# save.experiment(df, file = "path/to/save/experiment")
## You can then do:
# read.experiment("path/to/save/experiment")
# or (identical):
# read.experiment("experiment", in.dir = "path/to/save/")

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.